Devices and methods for biological sample preparation

ABSTRACT

Methods and devices for biological sample preparation and analysis are disclosed. A device may have a linear or circular arrangement of containers, with a connecting structure such as a bar or disk. Fluidics channels between containers allow the performance of different techniques for sample preparation, such as lysing, washing and elution. Different functional elements, such as grinders or mixers, may be attached to the containers.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional PatentApplication No. 61/722,355, filed on Nov. 5, 2012, and U.S. ProvisionalPatent Application No. 61/722,326, filed on Nov. 5, 2012, is acontinuation-in-part of U.S. patent application Ser. No. 13/407,644,filed on Feb. 28, 2012, and may be related to U.S. patent applicationSer. No. ______ “DEVICES AND METHODS FOR BIOLOGICAL SAMPLE-TO-ANSWER ANDANALYSIS” (Attorney Docket P948-USCIP2), U.S. patent application Ser.No. ______ “METHODS OF FABRICATION OF CARTRIDGES FOR BIOLOGICALANALYSIS” (Attorney Docket P925-USCIP), U.S. patent application Ser. No.______ “INSTRUMENTS FOR BIOLOGICAL SAMPLE PREPARATION DEVICES” (AttorneyDocket P1323-US), U.S. patent application Ser. No. ______ “INSTRUMENTSFOR BIOLOGICAL SAMPLE-TO-ANSWER DEVICES” (Attorney Docket P1325-US),U.S. patent application Ser. No. ______ “PEN-SHAPED DEVICE FORBIOLOGICAL SAMPLE PREPARATION AND ANALYSIS” (Attorney DocketP948-USCIP3), filed on even date herewith, the disclosure of all ofwhich is incorporated herein by reference in their entirety.

TECHNICAL FIELD

The present disclosure relates to biomolecular analysis. Moreparticularly, it relates to devices and methods for biological samplepreparation.

SUMMARY

In a first aspect of the disclosure, a device is described, the devicecomprising: a top structure, a bottom structure, and a connectingstructure, wherein the connecting structure connects the top structureto the bottom structure, and wherein the top structure comprises a firstplurality of containers, each container of the first plurality ofcontainers having: a top opening, wherein the top opening has a sealingelement which can slide inside the container while substantiallymaintaining a seal; a central part; a bottom opening; at least two portsin at least one container of the first plurality of containers, the atleast two ports comprising a first port configured for air venting; asecond port configured for fluid insertion; a sealing cap for each port;the bottom structure comprises a second plurality of containers, eachcontainer of the second plurality of containers having a top opening; acentral part; a bottom opening, wherein the bottom opening has a sealingelement; and the connecting structure comprises at least one fluidicschannel; a supporting element which can slide, rotate or move within aplane, thereby establishing a fluidics connection, through the at leastone fluidics channel, between the bottom opening of at least onecontainer of the first plurality of containers and the top opening of atleast one container of the second plurality of containers, whilesubstantially sealing other bottom openings of the first plurality ofcontainers and other top openings of the second plurality of containers.

BRIEF DESCRIPTION OF DRAWINGS

The accompanying drawings, which are incorporated into and constitute apart of this specification, illustrate one or more embodiments of thepresent disclosure and, together with the description of exampleembodiments, serve to explain the principles and implementations of thedisclosure.

FIG. 1 depicts an exemplary sample preparation device.

FIG. 2 illustrates an exemplary sample moving bar.

FIG. 3 illustrates some examples of injection ports and their operation.

FIG. 4 illustrates an exemplary sample preparation device with anadditional inlet cylinder on the side.

FIG. 5 shows the upper half of an exemplary device.

FIG. 6 illustrates an exemplary side view of a sample preparationdevice.

FIG. 7 illustrates an exemplary sample-to-answer device.

FIG. 8 illustrates a top view of a sample-to-answer device.

FIG. 9 illustrates an exemplary sample-to-answer device.

FIG. 10 illustrates an exemplary sample-to-answer device.

FIG. 11 illustrates a side entry port component.

FIG. 12 illustrates an exemplary cartridge with a reaction chamber.

FIG. 13 illustrates several views of an exemplary cartridge.

FIG. 14 illustrates a bottom view of an exemplary cartridge.

FIG. 15 illustrates an exemplary cartridge with three reaction chambers.

FIG. 16 illustrates an exemplary cartridge with a capillary, in crosssectional view.

FIG. 17 illustrates an example of a cartridge with reagents for opticaldetection.

FIG. 18 illustrates the exemplary cartridge of FIG. 17, with fluidpresent in the reaction chamber.

FIG. 19 illustrates another embodiment of detection based on totalinternal reflection.

FIG. 20 illustrates an exemplary cartridge with a fitted metal plateconnection.

FIG. 21 illustrates an exemplary method of fabrication for a curing anadhesive while protecting reagents applied to a surface inside areaction chamber.

FIG. 22 illustrates an exemplary reaction chamber with inlet and outletor vent ports.

FIG. 23 illustrates a circular embodiment of a cartridge with severalreaction chambers or reservoirs.

FIG. 24 illustrates an exemplary circular sample-to-answer device.

FIG. 25 illustrates a side view of the device of FIG. 24.

FIG. 26 illustrates a top view of the device of FIG. 24.

FIG. 27 illustrates a bottom perspective view of the device of FIG. 24

FIG. 28 illustrates a bottom view of two different sets of containerstructures.

FIG. 29 illustrates an example of two bottom sets of containerstructures.

FIG. 30 illustrates an exemplary connecting disk of a circular device.

FIG. 31 illustrates an exemplary rod to control a connecting disk.

FIG. 32 illustrates an exploded view of an exemplary circularsample-to-answer device.

FIG. 33 illustrates exemplary sealing rings.

FIG. 34 illustrates different possible features of container structures.

FIG. 35 illustrates different possible elements of a sliding bar.

FIG. 36 illustrates one embodiment of a container arrangement.

FIG. 37 illustrates an embodiment of a sample insertion container.

FIG. 38 illustrates an exemplary operation of a sample preparationdevice.

FIG. 39 illustrates an elution process.

FIG. 40 illustrates an exemplary sample-to-answer device with reactioncartridges attached.

FIG. 41 illustrates an exemplary sample-to-answer device configured forcapillary electrophoresis.

FIG. 42 illustrates an exemplary sealing arrangement between a sampleholder and a container structure.

FIG. 43 illustrates an exemplary sealing arrangement in details.

FIG. 44 illustrates some details of an embodiment of a sample-to-answerdevice.

FIG. 45 illustrates an exemplary set of cylinders which a protectingstructure.

FIG. 46 illustrates an exemplary sample insertion attachment forpipettes.

FIG. 47 illustrates an exemplary embodiment of a reaction cartridge.

FIG. 48 illustrates a top cross sectional view of an exemplary opticalanalysis instrument.

FIG. 49 illustrates a perspective view of an exemplary optical analysisinstrument.

FIG. 50 illustrates another perspective view of an exemplary opticalanalysis instrument.

FIG. 51 illustrates some details of an exemplary optical analysisinstrument.

FIG. 52 illustrates one embodiment of a cartridge housing.

FIG. 53 illustrates one embodiment of a cartridge housing, in differentviews.

FIG. 54 illustrates an exemplary sample preparation instrument.

FIG. 55 illustrates an exemplary motorized structure for asample-to-answer instrument.

FIG. 56 illustrates another view of the motorized structure of FIG. 55.

FIG. 57 illustrates some components of a sample-to-answer instrument.

FIG. 58 illustrates some details of the sample-to-answer instrument ofFIG. 57.

FIG. 59 illustrates an alternative view of the instrument of FIG. 57.

FIG. 60 illustrates a top view of the instrument of FIG. 57.

FIG. 61 illustrates a detailed view of an exemplary optical structure.

FIG. 62 illustrates an exemplary pen-shaped device.

FIG. 63 illustrates different fabrication methods for a reactionchamber.

DETAILED DESCRIPTION

The methods, devices and systems of the present disclosure relate to thepreparation and analysis of biological samples. For example, a portabledevice in the present disclosure may be able to accept a biologicalsample, such as blood or other human bodily fluid, and prepare thesample for further processing, for example by extracting nucleic acid orother target analyte of interest. Another portable device may alsocontain one or more reaction chambers, where a specific reaction cantake place after the sample has been prepared in the rest of the device.For example, the device may be able to prepare a biological sample andthen perform polymerase chain reaction (PCR). A system in the presentdisclosure may be an automated instrument that can accept a portabledevice such as those described in the present disclosure. The system maybe able to operate the portable device in an automatic rather thanmanual manner. The system may also comprise additional instruments thatcan analyze the sample, for example by optical techniques.

One example of procedures that can be executed through the devices andsystems of the present disclosure is polymerase chain reaction.

Polymerase chain reaction (PCR) is a critical technique in the detectionand amplification of nucleic acid products. However, before PCR can beperformed, DNA must be liberated and purified from serological samples.While there are chemical kits that can be used to perform both lysis andnucleic acid purification, such methods require significanttime-intensive and highly-skilled technical labor to implement. Thepresent disclosure describes several instruments and procedures thatperform these tasks in a way that results in significant cost- andtime-savings.

As known to the person skilled in the art, lysis comprises breaking downthe cell walls or membranes, thereby causing the liberation ofintracellular molecules.

PCR, and other techniques, are often only available through the use ofexpensive instruments or qualified operators. The systems and devices ofthe present disclosure can have the advantage of being portable and ofbeing cheaper and easier to operate than more traditional realizations.These advantages can allow their use in less technological areas of theworld, thereby enabling their use for disease detection, for examplemalaria detection.

The present disclosure also describes methods of operation of suchdevices and systems, as well as methods of fabrication for said devices.

FIG. 1 illustrates an embodiment of a fluidics device of the presentdisclosure for sample preparation. A housing (105) provides a supportingstructure for the various components of the device. For example, housing(105) and other components may be fabricated with transparent acrylicmaterials or other kinds of plastic materials. A number of cylindricalstructures, containers, container structures, reservoirs or cylinders(110) are affixed to the housing (105). The cylinders (110) may haveplungers (115) or other similar sealing structures that permit themovement of fluids into and out of the cylinders (110). As the personskilled in the art will understand, plungers (115), or other similarstructures, operate in a manner similar to a syringe. The diameter andsize of the cylinders (110) may be different. For example, sevencylinders (110) are visible in FIG. 1, all of similar size, exceptelution cylinder (120) which in this example is smaller. As describedpreviously (U.S. patent application Ser. No. 13/407,644, incorporatedherein by reference in its entirety), each cylinder (110) may have adifferent function. For example, a sample may be inserted in a firstcylinder (125), subsequently moved onto a lysing solution or buffercylinder (130), then in a washing cylinder (135) and finally in anelution cylinder (120).

The cylinders (110) may contain different solutions as required by thetechnique being applied to the biological sample. For example, solutionsmay comprise a lysing solution, water or other solvents, elutionbuffers, and PCR-related solutions and solvents. A lysate solution maybe moved from one cylinder to the next through the manual or automaticoperation of the plungers (115). The top plungers (140) and the bottomplungers (145) may be operated in an appropriate sequence to push theliquid up or down the cylinders (110), passing through the samplecontainer (150).

The sample container (150) may be, for example, a DNA binding matrix.The sample container (150) may be connected with cylinders (110) throughopenings (155) that allow the passage of fluids. The sample container(150) may be moved between the cylinders (110) by a horizontal slidingmovement, manually or automatically operated, of a bar (160).

In some embodiments, the bar (160) may be flexible, while the openings(155) are rigid. The flexibility would allow the bar (160) to slide inthe housing (105) while providing a waterproof seal at each opening(155). In other embodiments, the bar (160) may be rigid, while theopenings (155) are flexible. For example, the openings (155) may haveO-rings. Other combinations may be used.

For example, FIG. 2 illustrates a crossectional view of a bar (205) witha sealing structure (210). The bar (205) may comprise, for example, aninner structure (215), such as an aluminum bar, coated with a slidinglayer (220). For example, the sliding layer (220) may be Teflon tape.

Devices such as that of FIG. 1 may be used for sample preparation, inother words for preparing a sample for further processing. For example,a device may be used to extract or isolate DNA, proteins or otheranalytes, from a biological sample. The analyte may be extracted in aremote location, and analyzed at a later time in a laboratory.

Portable instruments may also be used, which accept the prepared sampleand apply further processing, for example thermal cycling for qPCR. Forexample, a sample may be extracted and prepared with a device such asthat of FIG. 1, and then inserted in a portable instrument which has aheater that can perform thermal cycling. As known to the person skilledin the art, thermal cycling can be employed for qPCR. The instrument mayalso have optical read-out capabilities. In some embodiments, theinstrument may have a contact heater operated with a solenoid, a housingwhere the sample is inserted, light source and detectors, and anynecessary waveguides to direct the light onto the sample. Multipledetectors may be used, for example each detector able to sense aspecific wavelength. The instrument may also comprise necessaryelectronic components for its control and operation. The solenoid may bea bistable solenoid: an electric pulse may activate the solenoid, inturn moving the heater in contact with the sample cartridge. Anotherpulse may activate the solenoid again, thereby moving the contact heateraway from the sample cartridge.

In some embodiments of the disclosure, devices are used for samplepreparation. In other embodiments, such devices are coupled to aninstrument which accepts a sample from the device and performs furtherprocessing such as thermal cycling and optical analysis. In yet otherembodiments, devices may perform sample preparation and additionallypossess a reaction chamber for specific techniques, for example qPCR. Inother embodiments, such devices with a reaction chamber may also becoupled to an instrument which accepts the sample and performsadditional processing such as thermal cycling and optical analysis. Forexample, an instrument may accept the PCR chamber of a PCR device andperform thermal cycling and cooling of the sample inside the PCRchamber, and additionally optical analysis. The instruments of thepresent disclosure are configured to accept the sample cartridges orreaction chambers of the corresponding devices. For example, a samplepreparation device may include a detachable qPCR reaction chamber, whichcan then be inserted into an instrument. Alternatively, a samplepreparation device may be inserted wholly into an instrument.

The devices for sample preparation, such as that in FIG. 1, may haveplungers or similar operational controls which are manually activated.Such plungers or similar controls may be operated automatically by aninstrument once the device is inserted into the instrument. Theinstrument may then have automatic means to push the plungers, forexample. In some embodiments, the instrument may have pistons which areautomatically controlled to push on the plungers of sample preparationdevices.

Devices and instruments which combine sample preparation and a techniquesuch as qPCR may be termed as sample-to-answer devices and instruments.Alternatively, the sample preparation step, and the qPCR step may bedone separately. In that case, instruments and devices may be specificto sample preparation. Other instruments and devices may be specific toqPCR. In other words, devices and instruments may be ‘samplepreparation’ devices and instruments, ‘qPCR’ devices and instruments, or‘sample-to-answer’ devices and instruments, when both ‘samplepreparation’ and ‘qPCR’ are performed. Other techniques may substituteqPCR, if such techniques can be effectively applied in the reactionchambers as described in the present disclosure.

Referring again to FIG. 1, cylinders 110 may have additional openings tofacilitate their operation. For example, cylinder (125) illustrates apossible level for a liquid (165) introduced in the cylinder (125).Above liquid level (165), openings (170) and (175) may be present.Opening (175) may be a vent hole, through which air can escape when aliquid is introduced. Opening (170) may be a sample injection hole orport, through which a sample can be introduced. A syringe or otherdevice may be used to introduce the sample. For example, a pipette or acapillary may be used. For example, finger pricks with attachedcapillary and hand-operated bulb exist which let an operator draw bloodand push it out of the capillary.

Opening (170) and (175) may be self-sealing, or have rubber caps orsimilar ways of closing. For example, opening (170) may be aself-healing or self-sealing injection port (septa).

In some embodiments, the injection port (170) may have an integrated, orremovable, adapter to allow the insertion of a pipette tip. In otherembodiments a capillary may be pre-attached to the injection port, foreasier operation.

FIG. 3 illustrates some examples of injection ports and their operation.

In FIG. 3, a capillary (305) may be attached to injection port (307). Aliquid solution may be present at a level (315) below injection port(310). Plunger (320) may be operated to contact liquid level (325) belowinjection port (330). In this way, the liquid cannot flow out of theinjection port (330) and operation of the device can continue. Forexample, plunger (335) may be pushed to move the liquid (340) out of thecylinder (345).

FIG. 4 illustrates an exemplary sample preparation device with anadditional inlet cylinder on the side. In some embodiments, cylinder(420) has an additional cylinder (405) on a side. Cylinder (405) mayalso have a sample injection port (410). Additionally, a filter (415)may be present. For example, a blood sample may be introduced incylinder (405), and blood cells may be filtered at filter (415), therebyintroducing plasma in cylinder (420). The plasma may then be processedby a sample preparation device or a sample-to-answer device, for exampleto test for malaria. While filters exist which can be attached to asyringe, they present a few disadvantages: for example, they may have asmall surface area and become easily clogged. An advantage of having afilter built-in into the device, such as filter (415), is that it can befabricated with a large surface area, thereby allowing fast filtering ofa biological sample.

FIG. 5 shows the upper half of an exemplary device. Circular recesses(505) may be present where O-rings can be inserted to provide a sealwhen the sample container is moved between cylinders. A plug-inconnector (515) may be present where, for example, a custom cylinder maybe inserted for specific applications. Alternatively, a capillary may beconnected to connector (515) to move the liquid sample to another deviceor instrument for further processing. For example, a capillaryconfigured to be used for optical detection may be attached to connector(515). In this way, optical detection can be applied to the sample inthe capillary, after processing in a sample preparation device or asample-to-answer device. In FIG. 5, a bottom view of the device alsoillustrates circular recesses (510).

FIG. 6 illustrates an exemplary side view of a sample preparationdevice. Although the cylinders (605) in FIG. 6 are placed in a line,other arrangements may be possible. For example, a circular arrangement.

FIG. 7 illustrates an exemplary sample-to-answer device, where a samplepreparation device (705), comprising several cylinders, is attached to areaction cartridge (710). Cartridge (710) may comprise, for example, aqPCR chamber, and it may be permanently attached to device (705), or maybe removable. In the example of FIG. 7, the reaction cartridge (710)comprises three separate compartments or reaction chambers (715),connected by microfluidics channels (720). A prism (725) may be part ofthe cartridge (710), to guide light onto the reaction chambers (715).The prism may be made of the same material of cartridge (710) and samplepreparation device (705), such as acrylic, PVC or other plasticmaterials.

FIG. 8 illustrates a top view of a sample-to-answer device, with areaction cartridge (804) with three compartments (805).

FIG. 9 illustrates an exemplary sample-to-answer device. The reactioncartridge (904) comprises, in this example, one reaction compartment(905). A prism (915) to guide light is part of the reaction chamber(905). Handles (910) are also part of the chamber (905), to facilitatehandling. The reaction cartridge (904), prism (915) and handles (910)may all be fabricated from the same material.

The cartridges of the present disclosure, such as cartridge (904) ofFIG. 9, may have a metallic back plate attached to the acrylic, PVC, orplastic material from which the rest of the cartridge is fabricated. Forexample, the metallic back plate may be made of aluminum. One purpose ofsuch metallic plate is to increase thermal exchange between the solutioninside a reaction chamber and an outside heater or cooler. It is knownto the person skilled in the art that in some reactions, for examplePCR, thermal cycling may be required. In such cases, it may beadvantageous to have a material with increased thermal conductivityrelative to plastic. Aluminum is safe to use with PCR and is cheaperthan noble metals, therefore it may be a good choice. Other metals mayalso be used, comprising noble metals. It is also known to the personskilled in the art that in certain situations it may be advantageous tofreeze-dry samples for later processing. It may also be advantageous tofreeze-dry the content of a cartridge, for example a cartridgecontaining solvents or reactive solutions which are meant to be part ofa preparation or analysis technique. For example, a solution withbinding molecules may be placed inside a reaction chamber andfreeze-dried for later use. In such cases, the use of a metallic backplate may be advantageous because of its enhanced thermal conductivity.

A metallic back plate may be bonded to a reaction cartridge by, forexample, the use of adhesives. One method comprises using a robot toreliably apply dots of adhesives at bonding sites of the reactionchamber and/or the metallic back plate. The two sides can then bepressed together with a constant and uniform pressure. The use ofautomated means of assembly, such as through a robot, allows a highdegree of repeatability and control. Alternatively, instead of applyingone dot of adhesive at a time, a mask perforated in an appropriatepattern may be used, and adhesive or other bonding agent may be sprayedor squeezed through the perforated mask, thereby printing adhesive dots,or an adhesive continuous line, along a desired pattern. Again, the twosides to be bonded can then be pressed together at an appropriatepressure. Such means of bonding enable an automated fabrication,suitable for lowering the price of each device and increase itsdeployment in areas where low cost is necessary for their establishment.

In several embodiments, the metallic plate is attached to the edges ofthe bottom part of the plastic cartridge; therefore the metal is indirect contact with the solution inside the chamber. The adhesive isplaced on the edges of the device. The adhesive may be cured asnecessary, without damaging the devices. Due to the different thermalexpansion coefficients of the metal and of the polymer materials (suchas PVC) used to fabricate the cartridge, it may be advantageous toreduce the contact area between the metal and the plastic components ofthe cartridge, in order to avoid any possible cracking of the cartridge.

Another advantage of a metal bottom plate is that it can have anincreased optical reflectivity, thereby increasing fluorescence andguide light in a more efficient way, for application in opticaldetection techniques.

Although several examples of the present disclosure refer to PCR and PCRreaction cartridges and chambers, the person skilled in the art willunderstand that different techniques may be related to the devices ofthe present disclosure. For example, a solution with enzymes for PCR maybe used in said devices, or lysing may be applied. Freeze-drying orlyophilization may be employed to store solutions or samples at roomtemperature, as their shelf life can be greatly increased once in driedform.

Lyophilization can be carried out on the cartridge before or afterbonding the metal and polymer parts. The metal part can help in fastlyophilization due to its thermal conductivity and large surface area.

After lyophilization of the reagents in either the metallic or polymericparts (or both) of the cartridge, room temperature bonding can be usedto cure the adhesive which bonds the metallic part of the cartridge tothe polymeric part of the cartridge.

Appropriate fabrication techniques can be used to protect thelyophilized reagents while bonding.

FIG. 10 illustrates an exemplary sample-to-answer device. A samplepreparation set of cylinders is visible (1005), as well as a reactioncartridge (1010). Adapters (1015) may be present on both sides of thedevice, to allow plugging into an instrument for automatic operation ofplungers, sample movement, thermal cycling and optical detection.

In several embodiments of the present disclosure, reaction cartridgesare described, which comprise reaction chambers. The reagents necessaryfor the desired technique to be performed can be prefilled in thereaction chamber in various forms. The reagents may be coated onto thewalls of the chamber or capillary, either covering the entire surface,or specific parts of the available surface.

Some reagents, such as qPCR reagents, may be lyophilized and coated onthe metal backplate. During operation of a device, the lyophilizedreagents may be reactivated by the appropriate solvent, e.g. water. Forexample, when the elution solution, containing the DNA of interest asprepared by the operation of the sample preparation device, fills areaction cartridge, the reagents are re-suspended and the reaction cantake place.

Reagents can also be lyophilized on the polymer side of the reactionchamber instead of on the metal side. Reagents can also be spotted onsurfaces depending on the application. Some applications are describedas following.

ELISA (enzyme-linked immunosorbent assay) is a technique that can beused with the devices of the present disclosure. In one embodiment, theantibodies with enzymes are immobilized on a surface of a reactionchamber (on the metal or polymer side). The sample (for example wholeblood) can be flowed through the cartridge, or be given some time sothat hybridization between the target analyte and the antibodies canoccur. A wash buffer can be used to flush out the sample and thecartridge can be used to detect the result. For example, the analytebound to the surface can be detected after the rest of the liquid sampleis flushed out.

For some samples, there is no need to flush the sample if, for example,optical detection can be carried out even in the presence of theremaining liquid sample. Alternatively to optical detection,electrochemical detection can be used using patterned electrodes on asurface of the chamber, either the metal or polymer (plastic) surface.To reduce the reaction time, the surface area can be increased bystructuring the surface, for example with nanopillars, fractal shapesand other surface treatments which can increase the interaction area. Aplastic surface can be patterned via injection molding or othertechniques. Increasing the interaction area can reduce the time forhybridization. The fluid can also be made to flow multiple times throughthe reaction chamber to increase the chance that the relevant moleculeswill attach to the binding sites. Flowing the fluid sample through thereaction chamber multiple times can reduce the total reaction time.

The cartridges of the present disclosure can also be used, for example,for immunoPCR to detect antigens. The patterning of reagents can be donesimilarly as to what described above. The capture agents (e.g.antibodies, aptamers) can be immobilized on the surfaces of the reactionchamber. In other embodiments, the binding of capture agents and targetstakes place outside of the cartridge and the PCR-ready solution isintroduced into the cartridge. This technique can be used to preservetime-sensitive analyte information at the point of care. Thus, theanalytes can be converted to amplicons via binding reactions. Sinceamplicons are often more stable than many analytes (like proteins,etc.), the PCR can be done later or at a different location. As known tothe person skilled in the art, the PCR has the ability to amplify theoriginal information and thus detect very low levels of analytes. qPCRcan be used to quantify the amplicons as well.

The reaction chambers of the present disclosure can also be used ashybridization chambers to allow detection via different techniques, suchas optical, electrochemical or others. For example, capillaryelectrophoresis is a viable detection technique. As known to the personskilled in the art, a capillary can be attached to a reaction chamberand electrophoresis is activated through a voltage difference. Thetarget analyte, such as DNA, will then move through the capillary as afunction of its size, thus allowing detection. For example, a negativevoltage can be applied to the metal base of the cartridge to repel theamplified DNA, which will then flow through an attached capillary. Thecartridge can thus integrate easily with capillary electrophoresisdetection without the need to fabricate additional electrodes. Asdiscussed previously, the reagents can be immobilized on a surface ofthe cartridge.

For the case of electrical detection, the metal surface or a part of it(with or without modification) can aid in electrical detection due toits high metallic conductivity. For example, electrodes may be patternedon the surface to employ cyclic voltammetry.

Among the possible applications of the devices and instruments of thepresent disclosure, the cartridges can be used to detect multiple DNAtargets as required in forensics and human identification.

During operation, when a sample, such as DNA, is introduced in areaction chamber, the metal backplate can help attract more DNA into thechamber. For example, an elute container attached to a reaction chambermay contain more liquid whose volume is larger than what can becontained the reaction chamber. To attract more DNA into the cartridge,a voltage can be applied to the metal backplate of the cartridge. TheDNA will then be attracted by the voltage difference between the chamberand the elute container, flowing through the elution liquid.

The above technique, using voltage to attract DNA, can also be used toenhance hybridization and reaction speed for various techniques whichuse patterning on the metal surface. Changing the voltage on the surfacecan also help in mixing (e.g. pulling and pushing DNA) andcapture/de-capture operations.

The reaction cartridge can also be used for complex biological sampleslike whole blood, for different uses such as pathogen detection.Heme-resistant enzymes can amplify the target in samples with wholeblood in it. Such enzymes can be utilized with the sample preparationand sample-to-answer devices of the present disclosure. For cleansamples, like spinal fluid (e.g. for meningitis tests) the sample can bedirectly used and thus the reaction cartridge with lyophilized reagentscan work on its own without sample preparation.

The cartridges of the present disclosure can also be used for solidphase PCR, possibly allowing significant multiplexing capabilities inone cartridge.

If the regents are coated on the polymer side, then evanescent waves canbe used to detect fluorescence, as the fluorophores are now very closeto the surface and they can be excited by TIR-based (totally internalreflection) waves. In order to limit noise and capture only thefluorescence signal by evanescent waves, the reaction chamber can bedried so that the electromagnetic rays that would be moving in the fluidhave minimal effect on the fluorescence. In other words, thefluorescence detection can be carried out with the fluid still in thechamber, in which case the signal detected will also comprise thefluorescence originating from the fluid. If, however, the chamber isemptied as well as possible, then little fluid will remain and thefluorescence signal will originate primarily from the target analytebound to the fluorophores coated on the walls of the chamber.

In other embodiments, the optical excitation angles of the light sourceand its collimation can be adjusted so that the evanescent wavefluorescence can be observed even for reaction cartridge filled withfluid.

The metal back plate of the cartridges can also be used for evanescentwave detection. For example a very thin SiO₂ (glass) coating can beapplied on the cartridge. The excitation light can then be guided withinthe coating. In other words, the fluorophores and the evanescent lightdetection can occur both on surfaces on the polymer surfaces of thechamber, or on the metal surface of the chamber. Alternatively, both thepolymeric and metallic surfaces could be coated with fluorophores orother binding reagents, at the same time.

When introducing samples in a device, their consistency may determinethe best way of their introduction. For example, some samples may bedenser than others, some liquid samples may be very viscous. Tofacilitate their introduction, as well as their mixing with any solutionpresent inside a device, certain components may be added to a device.For example, FIG. 11 illustrates a side entry port, similar to thatdepicted in FIG. 4. Referring to FIG. 11, a screw or mixer or screw pumpelement is visible (1105), whose purpose is to push the liquid forward.Element (1105) may also facilitate the mixing of a sample introducedthrough the port (1115), with the liquid already present in the device(1120). Element (1115) may be configured to move through cylinder (1120)when a liquid is introduced, up to an extended position (1110). As it isknown to the person skilled in the art, a similar technique is used inthe field of injection molding.

FIG. 12 illustrates an exemplary cartridge with a reaction chamber. Suchcartridge may be fabricated with a polymer, such as PVC, or otherplastic materials, and may comprise a metal backplate.

The cartridge of FIG. 12 comprises an inlet port (1205) and an outletport (1210) or vent. For example, as the sample is introduced throughport (1205), air is displaced through vent (1210). The solution presentin the reaction chamber (1215) can also be removed through port (1210).As discussed above, the cartridge comprises a metal backplate (1220),bonded to the polymer side through an adhesive (1225). The cartridge mayalso comprise handles (1230). The cartridge may also comprise a prism(1235) to focus and distribute light onto the reaction chamber (1215)when an optical detection technique is carried out. Inlet port (1205)may also be attached directly to a sample preparation device. Forexample, FIG. 10 displays an exemplary cartridge (1010) attached to asample preparation device (1015) thereby forming a sample-to-answerdevice.

FIG. 13 illustrates several views of an exemplary cartridge. Aperspective view (1305), a top view (1310), a front view (1315) and aside view (1320). As visible in the side view (1320), a metal back plate(1330) is bonded to the polymeric part (1335) of the cartridge. Theprism (1335) can be spaced away from the back plate (1330) in order todecrease the total surface bonding area between the metal element (1330)and the rest of the cartridge. By having a reduced surface area, lessstress is potentially applied to the cartridge, for example during achange of temperature due to different expansion coefficients. In otherembodiments, a cartridge may comprise more than one prism, in order toaccept optical inputs from multiple light sources. In some embodiments,the metal back plate (1330) may be coated with various substances suchas glass, parylene, polyimide, silicone etc. via spray coating, thermalevaporation, sputtering, physical vapor deposition and many otherprocesses. As understood by the person skilled in the art, siliconecoatings can be applied to needle syringes as well. The purpose of suchcoatings is to increase biocompatibility of the metal surfaces, as somemetals are toxic to the enzymes used as reagents in several techniquessuch as qPCR.

In some embodiments, reflective aluminum (for example manufactured byAnomet) can be used for the metal back plate of a cartridge, as it isPCR compatible. Such reflective aluminum can be coated via vacuumprocesses and has low cost and good optical properties.

The polymer part of a cartridge can be molded into light-guidingstructures such as lenses, concentrators etc. If the cartridge is madeof COC (cyclic olefin copolymer) or COP (cyclic olefin polymer) then theoptical properties of these materials can be used advantageously asrequired by optical techniques.

A very thin metal foil can be used as a metal base for a cartridge, forexample similar to aluminum foil as used in food packaging. Such foilcould be used, for example, to increase optical reflectivity. Formechanical support, the foil could be applied to a back plate, such as apolymeric back plate, or a metallic back plate of a different metal. Thesheet metals used in cans, such as those for beverages, can also be usedas a metal base for a cartridge. Such sheet metals can have a polymercoating on the inner surface.

FIG. 14 illustrates a bottom view of an exemplary cartridge with anexemplary shaded area (1405) which illustrates as a bonding area betweena polymer cartridge and a metal back plate.

FIG. 15 illustrates an exemplary cartridge with several reactionchambers, both in perspective view (1505) and top view (1510). Thecartridge may comprise, for example, three reaction chambers (1515)connected by microfluidics channels (1520), and an optical prism (1525).Prism (1525) may be configured to distribute, guide and/or focus lightover all of the three chambers (1515) simultaneously, for opticaldetection applications. By carefully controlling the amount of fluidintroduced in a cartridge, it is possible to only fill the threechambers (1515) while leaving the connecting channels (1520) empty, orfilled with air. In this way, the three chambers (1515) remain separatedand their content will not mix. A different reaction can therefore beapplied in each of the three chambers (1515), if desired. Suchseparation with air can be achieved in different embodiments of thecartridges of the disclosure, by using a similar principle of operation,as can be understood by the person skilled in the art.

FIG. 16 illustrates an exemplary cartridge with a capillary, in crosssectional view. The cartridge comprises a polymer part (1605) and ametal back plate (1610). The outlet is linked to a capillary (1615). Thecapillary's function has been described above in the present disclosure,and comprises, for example, flowing the liquid sample from a cartridgeto another container, or even performing detection techniques throughthe capillary, such as capillary electrophoresis. For example, apositive voltage may be applied at the capillary (1620), and a negativevoltage may be applied to the metal plate (1610). For example, DNA maybe attracted by the voltage difference, flowing in the capillary (1615)with different speed depending on the size of the DNA. Thus, forexample, different DNA parts may be spaced along the capillary (1615)through the voltage difference.

FIG. 17 illustrates an example of a cartridge with reagents for opticaldetection. The cartridge comprises a polymer body (1705) and a metalplate (1710). Reagents (1715) may be attached to the walls of thecartridge, and light (1720) may be guided through total internalreflection, for example originating from a light source and guidedthrough a prism, such as prism (1235) of FIG. 12. Referring again toFIG. 17, an evanescent field (1725) will be present due to the lightrays (1720), as understood by the person skilled in the art. Thereagents (1715) will bind, or not, with the target analyte present, ornot, in a liquid sample. The presence or absence of the target analyteat the reagent sites (1715) can be detected, through the evanescentfield (1725) of light rays (1720). In some embodiments, a voltage mayalso be applied at plate (1710), for example to attract the targetanalyte inside the reaction chamber through an inlet port.

FIG. 18 illustrates the exemplary cartridge of FIG. 17, with fluid(1805) present in the reaction chamber.

FIG. 19 illustrates another embodiment of detection based on totalinternal reflection, with reagent sites (1905) and evanescent waves(1910), where the reagent sites (1905) are placed on the bottom of acartridge, on the metal plate (1920) side. In some embodiments, themetal plate (1920) may be coated with a transparent coating (1915)acting as a waveguide to allow the total internal reflection of light(1925).

FIG. 20 illustrates an exemplary cartridge with a fitted metal plateconnection. In this embodiment, a cartridge comprises a polymer side(2005) and a metal plate (2010), where the polymer side (2005) isfabricated so as to have a snap-on shape which fits the metal plate(2010). In such a way, less adhesive or even no adhesive may benecessary to bond the polymer side (2005) with the metal side (2010).

FIG. 21 illustrates an exemplary method of fabrication for a curing anadhesive while protecting reagents applied to a surface inside areaction chamber. A cartridge comprising a polymer side (2102) and ametal plate (2103) has a layer of coated reagents (2120) inside thereaction chamber (2104). In order to cure the adhesive (2115), in someembodiments light rays (2125) need to be directed at the adhesive(2115). In order to protect reagents (2120) from the light rays (2125),a mask (2105) supported by a transparent plate (2110) may be used toblock certain rays while allowing other rays to cure the adhesive(2115).

FIG. 22 illustrates an exemplary reaction chamber with inlet and outletor vent ports. In some embodiments, a reaction cartridge may comprise areaction chamber (2205) connected through microfluidics channels (2210)to an inlet port (2215) and an outlet port or vent port (2220). Suchports (2215, 2220) may be placed on the same side of a cartridge forease of access.

FIG. 23 illustrates a circular embodiment of a cartridge with severalreaction chambers or reservoirs. A circular structure or cartridge(2305) may comprise several chambers or reservoirs able to containliquid samples, for example four chambers (2310). Light rays (2315),originating from a light source, may be directed at one of the chambers(2310). The circular cartridge (2305) may be configured so as to allowinternal reflection of light rays (2320) so that a single light sourcecan illuminate all the chambers (2310). In other embodiments, thecircular structure (2305) may rotate in order to illuminate one at atime each of the chambers (2310). In FIG. 23, an inlet port (2325)connects to the chambers (2310) through channels (2330).

FIG. 24 illustrates an exemplary circular sample-to-answer device. Anarrangement of cylinders (2405) or other similar container structurescan be arranged in a circular manner. This arrangement may have theadvantage of having a compact shape. The structures (2405) may havedifferent shape or size, depending on the specific application. Forexample, an elution structure (2410) may have a smaller volume as oftenthe elution requires a smaller volume of liquid as it will be understoodby the person skilled in the art. In FIG. 24 a cartridge (2415) is alsopresent, for example for PCR techniques. The different components of thedevice of FIG. 24 can be similar as to those previously described in thepresent disclosure, with a difference being the circular arrangementvisible in FIG. 24.

FIG. 25 illustrates a side view of the device of FIG. 24. The device ofFIG. 25 comprises a top set of cylinders (2505), a bottom set ofcylinders (2515), and a central disk (2510) connecting the top (2505)and bottom (2515) set of cylinders.

FIG. 26 illustrates a top view of the device of FIG. 24. In FIG. 26 aset of cylinders (2605) is visible, as well as a cartridge (2610), thecartridge (2610) comprising a reaction chamber (2615) and a prism(2620).

FIG. 27 illustrates a bottom perspective view of the device of FIG. 24.In FIG. 27, a set of cylinders (2705) is visible, as well as a cartridge(2710). In the following, some component parts of the device of FIG. 24are described in more details.

FIG. 28 illustrates a bottom view of two different sets of containerstructures. A first set of containers (2805) is shown from a bottomview. A second set of containers (2810) is shown from a top view. Thesecond set of containers (2810) may comprise one or more containerswhich are not in cylindrical shape. For example, containers (2815) havea flattened shape. This shape allows for a higher surface area internalto the containers (2815). Such higher surface area may be advantageousfor several reasons, for example increase area to allow for increaserate of reaction for the target analyte in a sample solution and thereagents coated on the surface. Another advantage may be increase areafor controlling the temperature of the solution. For example, anexternal heater (2820) may be attached to an external surface of acontainer (2815), allowing for thermal cycling, heating or cooling,depending on the requirements of the technique used.

In some embodiments, different thin films can be used as heaters. Forexample, laminates like DuPont Pyralux APR (embedded resistor laminate)can be used. In some embodiments, they can be bonded to a metallicsurface using thin dry film adhesives, for example as those used in theprinted circuit board industry as understood by the person skilled inthe art.

A temperature sensor can also be deposited, for example on a kaptonlaminate. The temperature sensor can be made, for example, withdeposited platinum, copper, nickel or other metals.

Copper tracks on a standard flexible laminate can also be used as aheater. The temperature sensor could also be fabricated with a copperlaminate. The resistance of sensor can be controlled as necessary bycontrolling the thickness of the conducting metal element.

In some embodiments, the heater can be a part of metal plate, withoutcomprising any polymer, in order to have increased total thermalconductivity. For example, if the base of a heater is metallic (forexample, aluminum or copper) then one side of the metal can be anodized,to render it electrically insulating. SiO₂ or other insulating coatingscan also be applied. In other embodiments, a nichrome heater could bedeposited as a heating element, while copper tracks can be deposited ascontacts. As understood by the person skilled in the art, current can bepassed through a metallic element to increase its temperature, in orderto act as a heater.

FIG. 29 illustrates an example of two bottom sets of containerstructures, from a top point of view. One set of containers (2905) isfor a sample preparation device. A container (2915) for collection ofthe prepared sample is visible. Another set of containers (2910) is fora sample-to-answer device, comprising a reaction cartridge (2920).

FIG. 30 illustrates an exemplary connecting disk of a circular device.Such connecting disk may correspond, for example, to element (2510) inFIG. 25. Referring to FIG. 30, the connecting disk structure (3005) isconfigured so as to slide horizontally, or move relative to the rest ofa device. A set of apertures (3010) are visible which correspond toapertures in the containing structures of the device, for examplecylinders (2910) of FIG. 29. In FIG. 29, apertures (2925) can beconnected by a connecting channel in the connecting disk, such aschannel (3015) in FIG. 30.

Referring to FIG. 30, channel (3015) can be used to connect containingstructures in the rest of the device. In this embodiment, the fiveapertures (3010) visible in FIG. 30 are not a part of connecting disk(3005) but are shown to explain the operation of this embodiment of thedevice. Channel (3015) is part of disk (3005), and by moving disk(3005), apertures (3010) can be connected by channel (3015), therebyallowing the movement of fluids between containing structures of adevice. A sample holder (3020), for example a DNA binding matrix, isshown as an example, at a site of one of the apertures of a containerstructure. By moving disk (3005), the sample holder (3020) may be movedbetween any of the five apertures (3010). In other embodiments, adifferent number of containing structures may be used.

In FIG. 30, the center (3025) of a device is shown to exemplify amovement of disk (3005). For example, disk (3035), which corresponds todisk (3005) before the movement, is moved in the direction indicated byarrow (3030). Disk (3035) is then now translated horizontally relativeto the apertures in the containing structures which are located, forexample, in a circular pattern (3040). Channel (3045), corresponding tochannel (3015) before movement of disk (3005), is now connecting twoadjacent apertures (3050). It will be understood by the person skilledin the art that different variations of size and shape and arrangementof the components similar to those described in the present disclosuremay be possible, and the examples here described are not intended as alimitation.

Disk (3005) may be moved by a variety of means, for example by a handleon a side of the disk, or by a rod attached to the bottom of the disk.For example, as visible in FIG. 31, a rod (3105) may be attached to thecenter of a disk (3110). A slot (3115) for a sample holder (such as aDNA membrane) is visible. The structure is shown in perspective view(3120) as well as side view (3125).

In an additional view (3130), a zoomed in view of slot (3115) isillustrated. Slot (3115) is configured to hold a sample holder in astable position, while allowing movement of fluid in and out of thesample holder as desired. Rod (3105) may be rotated or moved in thehorizontal plane of the connecting disk (3110). Slot (3115) may have acountersink shape to facilitate holding of the sample container, such asthe DNA membrane.

As understood by the person skilled in the art, the devices andinstruments of the present disclosure can be used for a variety oftechniques, for example nucleic acid sample preparation. Nucleic acidsample preparation is a highly labor intensive and time consumingprocess requiring multiple steps to collect DNA and/or RNA frombiological materials such as whole blood, blood serum, buffy coat,urine, feces, semen, saliva, sputum, nasopharyngeal aspirate, spinalfluid, and tissue from biopsies. Nucleic acid isolated from saidbiological materials can also comprise the endogenous nucleic acid fromthe organism from which the sample is derived and any foreign (viral,fungal, bacterial or parasitic) nucleic acid.

To simplify the steps in the sample preparation process, the presentdisclosure comprises the use of a fluidic cartridge for extraction andpurification of nucleic acid from biological material. This inventioncan offer the advantages of being rapid, low cost, reliable, andportable, thereby yielding high purity DNA and/or RNA that can then beused as a reagent in molecular biological reactions. The presentdisclosure can support a range of applications and extraction protocols;and can comprise both automated and manual operation.

One of the first steps in many laboratory tests is the isolation andpurification of nucleic acid, which is essential to a wide variety ofbiotech, research, forensic, and clinical applications. These procedurescan consume considerable time, labor and costly materials. In order toensure easy and inexpensive point-of-care diagnostics, it would beadvantageous if little or no sample preprocessing at the bench wererequired.

The devices of the present disclosure can simplify sample preparation bycombining all of the complex protocols of DNA and/or RNA extraction intojust a few steps. The steps for isolating nucleic acid from biologicalmaterials comprise (1) take in the biological sample via the sampleinput port; (2) mix sample with lysis buffer and lyse the nucleiacid-containing cells, tissue, etc.; (3) bind nucleic acid to porousnucleic acid binding membrane; (4) remove contaminants with wash buffer;(5) air dry; and (6) elute nucleic acid in buffer or water.Concentration and purification of nucleic acid can makes each sampleready for downstream molecular diagnostic testing with yields comparableto industry-standard methods.

In several embodiments of the disclosure, the sample holders are basedon a porous nucleic acid binding membrane which can be embedded in asingle-use bar or connecting disk. The bar slides back-and-forth alongthe center of the cartridge and aligns the nucleic acid binding membranewith the opening of each port pair. Alternatively, the disk can move ina plane for a similar purpose. The bar or disk can be fitted withnucleic acid binding membranes from various types of commerciallyavailable DNA/RNA extraction kits, thus allowing the fluidic cartridgeto extract from a wide range of source comprising: Human genomic DNAfrom blood, saliva, or semen; DNA and RNA from bacteria such asStaphylococcus aureus and Streptococcus pyrogenes; DNA and RNA fromblood-borne microbes such as B. anthracis; Microbial DNA in culture,urine and more for such microbes as B. anthracis, Adenovirus, and E.coli; Viral RNA in culture, urine and more for Herpes Virus I, andChlamydia trachomatis; Influenza A and B from nasal aspirate andrespiratory swab samples in viral transport media.

The sample preparation cartridge's flexible protocol can work withchaotropic salt chemistry and can be designed to handle a range ofsample volumes, for example in the range 50 J.LL-10 mL). Additionally,in order to work directly with human whole blood samples, whole bloodfilters can be incorporate into the device.

The sample preparations and sample-to-answer devices of the presentdisclosure can comprise complementary port pairs on both the bottom andtop half of a device, as visible for example in FIG. 27. Each of the topcontainers can contain reservoirs for the appropriate buffer solutionsfor each step of a desired technique. The containers can be pre-filledwith the solutions or solutions can be added manually during each step.In several embodiments, the bottom half of the devices can containsports which act as waste reservoirs for the buffer solutions.

In some embodiments, a sample is first mixed with a high-salt lysisbuffer (which could contain magnetic beads, colloidal gold particles,silica, etc.) to chemically or mechanically lyse the cells. Mixing canbe achieved by external ultrasonic or vibration coupled to the insertionport of the device. Additionally, the reservoir could have a heatersurrounding it to perform thermal lysis; or also include a magneticelement to perform magnetic lysis.

The mixture can then be passed through a nucleic acid binding matrixusing a piston/actuator mechanism. Fluid can flow through the nucleicacid binding membrane. High pressure can be applied allowing rapidoperation. By matching the shape of a piston or plunger to thereservoir, •the piston will force the majority of the fluid to thecomplimentary port on the other side; thus minimizing the dead volume.Additionally, the fluid can be pushed/pulled back through the membranebetween pairs of ports. This allows multiple passes through the nucleicacid binding membrane which will enhance binding of the nucleic acid tothe membrane. The pistons can also be moved slowly or stopped to allowgreater binding time.

Once the nucleic acids are bound to the membrane, the bar or disk canslide to the next set of ports to perform a washing step. Washing thenucleic acid can encompass one cycle or multiple cycles to furtherenhance binding of DNA and/or RNA to the membrane and for efficientremoval of contaminants.

Next, the bar can move to the next set of ports to perform an air dryingstep. By moving the pistons up and down inside the ports, air can beaspirated through the nucleic acid binding membrane and dry themembrane. Furthermore, a heating element can also be incorporated tohelp dry the membrane faster and evaporate off any residual wash buffer.

Further, the isolated nucleic acids can be eluted off the membrane inbuffer or water solution. A heating element can also be incorporatedaround the port to control the temperature of the elution buffer andmaximize the release of nucleic acid. The eluent containing the releasednucleic acid can be captured in a PCR tube attached to the sample outputport or directly injected into a molecular diagnostic device foranalysis.

The devices of the present disclosure can be injection molded,compression molded, 3D printed or rapid prototype printed from numeroustypes of materials, including but not limited to thermoplastic, metal,glass, and elastomers.

Several embodiments of the devices of the present disclosure can allowfor manual and automated operation. For manual operation, these devicescan be run completely by a hand-held syringe, plunger, piston, orsimilar element. Insertion ports can be configured for direct insertionof syringes, needles, pipette tips or luer lock tips.

The devices of the present disclosure may have applications in the areasof analytical chemistry, forensic chemistry, microfluidics andmicroscale devices, medicine, and public health. They may be useful fora wide variety of applications including fluid manipulation, diagnosticand analytical test, chemical and biological analysis, food safety, drugtesting, fluid metering and others.

FIG. 32 illustrates an exploded view of an exemplary circularsample-to-answer device, comprising a top set of containers (3205), aconnecting disk (3210), a bottom set of containers (3215) and a reactioncartridge (3220).

FIG. 33 illustrates exemplary sealing rings (3305) which provide sealingbetween a set of containers and a connecting disk.

FIG. 34 illustrates different possible features of container structures.A container (3405) may be used for the sample, lysate or mixture.Containers (3410) and (3415) may be for different washes. Container(3420) may be for elution. In some embodiments, the bottom containersmay have air-permeable membranes (3425), elastic pistons (3430) orflexible reservoirs (3435). For example, reservoirs (3435) may beflexible and may be squeezed by hand, similarly to a rubber balloon. Theair-permeable membranes (3425) may be useful for drying as the membranes(3425) can allow air through, but not fluids or DNA. In someembodiments, hot air can be directed onto the air-permeable membranes(3425) in order to dry the content of a container. The elastic pistons(3430) may comprise a spring attached to a seal. As fluid is inserted ina container, the spring is pushed back, and when pressure is not appliedagainst it anymore, the spring will push back against the fluid in thecontainer, thereby enabling its movement thanks to the elastic energystored in the spring of the elastic piston (3430).

Container structures of the devices of the present disclosure may beused, for example, for homogenization, lysis, filtration, mixing,ultrasonic lysis, debubbling, or protein filtering. The containers mayalso be empty. Similarly, the sliding bars or connecting disks asdescribed in the present disclosure, may house elements which canperform different functions other than holding a sample. For example,FIG. 35 illustrates different possible elements of a sliding bar.Different sample holders may be used (3505), for example differentmembranes. Filters, mixers or homogenizers (3507) may also be used, oreven empty channels (3510) to connect different containers of a deviceand allow the movement of fluids between the container structures.

In some embodiments, additional containers may be added, for example asillustrated in FIG. 36. A first container (3605) maybe used, forexample, to insert a fluid in a second container (3610). For example,ethanol may be used to enhance binding. Alternatively, the secondcontainer (3610) may also be filled with ethanol or other fluid.

FIG. 37 illustrates an embodiment of a sample insertion container forthe sample-preparation or sample-to-answer devices of the presentdisclosure. For example, a side container (3705) may house a grinderelement (3710). This grinder element (3710) may be used to grind solidsamples, or liquid samples which container solid particles or semi-solidparts. The grinder element (3710) may be operated, for example, byrotating a handle (3715). The side container (3705) comprises a sampleinsertion port (3720) and may comprise a filtering element (3725), forexample an element with a sharp teethed structure which can aid ingrinding or mixing a sample.

FIG. 38 illustrates an exemplary operation of a sample preparationdevice. A lysate, sample or mixture may be moved from one container(3805) to the opposite one (3810), with the fluid flowing through a DNAmembrane (3815). Another functional element (3820) may be present, forexample a filter, mixer, or lysing element, configured to work with alysing technique, such as electric, magnetic, mechanical, or ultrasoniclysing.

Alternatively, a sample may be moved from a container (3825) to theopposite one (3830) through an empty channel opening (3840), while theDNA membrane (3835) has been rotated to a different position. Othercontainers (3845) may contain, for example, a washing solution, asunderstood by the person skilled in the art.

FIG. 39 illustrates an elution process, where the fluid, after previousprocessing in the sample preparation device, undergoes elution and ismoved from one container (3905) to the opposite one (3910).

FIG. 40 illustrates an exemplary sample-to-answer device with reactioncartridges attached (4005).

FIG. 41 illustrates an exemplary sample-to-answer device configured forcapillary electrophoresis. A capillary (4105) attached to a capillaryelectrophoresis instrument (4110) enables the separation of biologicalspecies through a voltage difference, as it is known to the personskilled in the art. A hybridization chamber (4115) is also visible. Acontainer (4120) can be configured to be used as a pump to move a fluidto a capillary electrophoresis buffer or a wash buffer forhybridization.

FIG. 42 illustrates an exemplary sealing arrangement between a sampleholder (4205) and a container structure (4210). For example, sealing canbe obtained with a sealing element (4215), such as an O-ring or a rubberprotrusion, and a secondary, or back up, rubber seal (4220).

FIG. 43 illustrates an exemplary sealing arrangement in details.Container structures (4305) are partially visible. A sealing element(4310), such as a rubber ring, is shown as detached for clarity. Slots(4315) correspond to the sealing element shape for better sealing.

FIG. 44 illustrates some details of an embodiment of a sample-to-answerdevice. An elution container (4405) which may be part of asample-to-answer device as described above in the present disclosure,can be tied, in this embodiment, to an additional container (4410), sothat they are both operated simultaneously. For example, the twocontainers (4405, 4410) may be operated by a single plunger (4415). Ifthe volumes of the two containers (4405, 4410) is accurately measured,then it is possible to determine and configure a desired ratio betweenthe fluids contained in both containers (4405, 4410). For example, incertain reactions it is necessary to arrange a precise ratio ofsolutions to be mixed in order for the reaction to be optimized. Bydetermining the ratio of the volumes of containers (4405, 4410), theirsolutions can be mixed in a desired ratio.

Elution container (4405) may move its liquid through a sample holder,such as a DNA membrane (4420). Subsequently, the fluids of containers(4405, 4410) can be mixed in a mixer (4425). Mixer (4425) may befabricated in different ways. For example, it may consist of twomicrofluidics channels. It is known in the art that the flow of liquidsin microfluidics channels is often laminar. Therefore, two liquids mayflow parallel to each other, in contact but actually without any mixingtaking place. Mixer (4425) may be configured, for example, to allow someturbulence in the flow in order for the liquids from containers (4405,4410) to mix.

The mixed solution coming out of mixer (4425) may then enter, forexample, a reaction chamber (4430), like that in a qPCR cartridge. Thetechnique of FIG. 44 may also be useful for other applications likeELISA or immunoPCR.

The necessary reagents may be lyophilized in the qPCR reaction chamber(4430) as described in the present disclosure. When the elute, whichcontains DNA, flows into cartridge (4430), the reagents may bere-suspended.

In one embodiment, the reagents comprise a Master Mix comprisingenzymes, fluorescent dyes, oligonucleotides etc. As known to the personskilled in the art, a PCR Master Mix is a premixed, ready-to-usesolution comprising, for example, Taq DNA polymerase, MgCl₂ and reactionbuffers at optimal concentrations for the efficient amplification of DNAtemplates.

The reagents may also be stored in liquid form or added before using thecartridge (4430). This may be useful in cases where lyohpilizaition isdifficult or where the reagents can be stored easily in a refrigeratedplace external to the sample-to-answer device.

In another embodiment, the reagents can be lyophilized outside of thechip, in a lower part of container (4410), separated by a partition to atop part of container (4410), the top part being filled with liquid,such as water, or a solution. In this embodiment, pushing the plunger(4415) breaks the container and the solution in the top part of thecontainer (4410) can rehydrate the reagents in the lower part of thecontainer (4410). The resulting solution is then pushed into the mixer(4425).

FIG. 45 illustrates an exemplary set of cylinders which a protectingstructure. The cylinders may be used in a sample preparation orsample-to-answer device, together with a connecting ring and a secondset of cylinders, as described for example in FIG. 32. Referring to FIG.45, this embodiment has an additional protective circular structure(4505) which can protect a connect ring. Other protective structures maybe added, such as covers or other seals over the plungers which operatethe cylinders, in order to prevent accidental activation of the plungersprior to their intended use.

FIG. 46 illustrates an exemplary sample insertion attachment forpipettes. For example, the insertion port of a cartridge (4605) may havea structure (4610) designed to fit a pipette tip, in order to facilitatethe use of a pipette.

FIG. 47 illustrates an exemplary embodiment of a reaction cartridge. Inthis embodiment, the top of a cartridge is fabricated with a flexiblepolymeric material (4705), mechanically similar to a plastic blister orballoon. The flexible top (4705) can be pierced by a syringe, or have anprebuilt opening, through which a sample fluid can be introduced,thereby inflating the chamber and expanding the flexible top (4705). Byusing a flexible top (4705), an air vent can be unnecessary.

In several embodiments of the present disclosure, the cartridges may befilled in fluids. For example, referring to FIG. 12, the reactionchamber (1215) can be filled from inlet port (1205), while air is ventedthrough outlet port (1210). Once the cartridge is sealed, thermalexpansion may occur due to an increase in temperature. The consequentincrease in pressure could damage or even crack open a cartridge. Toobviate this potential problem, care can be taken to only fill thereaction chamber (1215), but leave empty the inlet and outlet channelsunderneath ports (1205, 1210). This can be done as the volume of areaction chamber can be accurately determined, and only a specificvolume of fluid is introduced. In such a way, air remains in thechannels leading to a reaction chamber. Since air can compress to agreater degree than fluid samples used in the cartridge of the presentdisclosure, then any increase in pressure will compress the air insidethe cartridge, acting as a protective pressure buffer which should avoidmechanical damage of a cartridge.

In several embodiments, the reaction cartridge has a metal back plate,as described previously in the present disclosure. For example,referring to FIG. 47, a metal back plate is illustrated (4710).

As understood by the person skilled in the art, some techniques relatedto the devices and methods of the present disclosure, comprise thereagents which are coated onto a surface of a reaction chamber containedin a cartridge. The reagents will bind with analyte targets of interestin a sample solution. In such cases, it can be advantageous to increasethe surface area where the reaction takes place. Such surface increasecan be achieved by patterning the inner surfaces of a reactioncartridge. For example, nanopillars or other microscopic structures maybe patterned onto a surface with methods which will be known to theperson skilled in the art, comprising micromolding, nanostamping,etching, and others. The increased surface area can acceleratehybridization or other reactions.

The polymer part of a cartridge can also be patterned to form pillars ofstructures to use the capillary effect to fill the fluid in thecartridge. Thus a reaction chamber can be filled only by capillaryaction. For example, there can be a reservoir to put blood from alancet, and the blood automatically enters the cartridge throughcapillary action.

In other embodiments the blood could be added to a buffer in a reservoirand the mixture can subsequently be pulled into a cartridge by capillaryeffect.

If the pillars or patterned structures are on a metallic surface, theycan also act as electrodes or other functionalized elements. There are awide variety of ways, as understood by the person skilled in the art, togrow pillar-like structures by electrochemical methods. Otherfabrication techniques may also be employed.

FIG. 48 illustrates a top cross sectional view of an exemplary opticalanalysis instrument (4800). For example, such instrument could be usedfor qPCR, and could be termed a qPCR instrument. Instrument (4800) maycomprise a cartridge housing (4805), where a reaction cartridge, such asa qPCR cartridge, may be inserted. Any cartridge as described in thepresent disclosure may be used in connection with an appropriateinstrument, such as instrument (4800). In some embodiments, a cartridgeis detachable from a sample-to-answer device, and therefore can beremoved from a device and inserted in an instrument, such as instrument(4800), for further processing.

Instrument (4800) may comprise a metal plate (4810), which can be movedby a bistable solenoid (4815), for example. Plate (4810) can be used asa support for the cartridge housing (4805), to position it in a correctposition for optical interrogation. In other embodiments, plate (4810)may comprise a heater plate which is moved into contact with cartridgehousing (4805) in order to be able to control the temperature of housing(4805), for example for thermal cycling in PCR.

Instrument (4800) may comprise plate (4820) as a structural supportelement which is fixed. Electronic boards may be housed in section(4825), to control automated elements in the instrument (4800), such asthe solenoid (4815).

Instrument (4800) may also comprise an optical element (4835) which cangenerate electromagnetic waves (such as light rays) at the desiredwavelengths in order to perform optical techniques on a sample inside acartridge in the housing (4805). Electromagnetic waves may be guided ona cartridge by a waveguide (4830). Instrument (4800) may comprise one ormore detectors, for example detector (4840), to detect electromagneticwaves exiting the cartridge, as will be understood by the person skilledin the art. Different light sources may be employed as element (4835),for example LEDs or lasers.

FIG. 49 illustrates a perspective view of an exemplary optical analysisinstrument, such as a qPCR instrument. Elements in FIG. 49 retain thesame significance as those similarly numbered in FIG. 48.

FIG. 50 illustrates another perspective view of an exemplary opticalanalysis instrument, such as a qPCR instrument. Elements in FIG. 50retain the same significance as those similarly numbered in FIGS. 48 and49.

FIG. 51 illustrates some details of an exemplary optical analysisinstrument, such as a qPCR instrument. Elements in FIG. 51 retain thesame significance as those similarly numbered in FIGS. 48, 49 and 50.

FIG. 52 illustrates one embodiment of a cartridge housing (5205),configured to accept and hold a cartridge (5210), in order to insert thecartridge and housing in an instrument, such as the optical analysisinstrument of FIG. 50.

FIG. 53 illustrates a side view (5201) and a top view (5202) of anexemplary cartridge housing (5205), configured to accept and hold acartridge (5210), in order to insert the cartridge and housing in aninstrument, such as the optical analysis instrument of FIG. 50. Elementsin FIG. 53 retain the same significance as those similarly numbered inFIG. 52. Referring again to FIG. 53, in some embodiments, plate (5215)may be configured to act as a heater.

FIG. 54 illustrates an exemplary sample preparation instrument (5400).In this example, the sample preparation instrument (5400) can acceptlinear sample preparation devices, such as device (5405), however inother embodiments a sample preparation instrument may accept circularsample preparation devices. Other shapes may also be used.

In FIG. 54, a linear sample preparation device (5405) can be inserted inthe sample preparation instrument (5400). A box (5410) may be used tohouse the different components. Rails (5415) may be attached to allowthe operation of a sliding door, in order to access the inside ofinstrument (5400), for example to insert the sample preparation device(5405), while protecting the instrument (5400) when it's not inoperation. Electronics (5420) may be used to operate the instrument(5400). Instrument (5400) may comprise a touchscreen (5425) for ease ofoperation. Instrument (5400) may comprise motors to actuate theplungers, or similar mechanisms, which operate a sample preparationdevice. For example, FIG. 55 illustrates an exemplary motorizedstructure for a sample-to-answer instrument, which can be used tooperate a circular sample-to-answer device. Similar arrangements may beused to operate sample preparation instruments, as both samplepreparation devices and sample-to-answer devices comprise containerswhich can be actuate through similar motorized arrangement.

The motorized structure of FIG. 55 comprises a motor (5505) for circularmovement of a supporting structure (5510). A linear actuator (5515) canbe attached to the supporting structure (5510), so that motor (5505) canrotate and align the linear actuator (5515) with the desired container(5520). The linear actuator (5515) can then be activated to operate aplunger (5525) or similar structure used to move fluid in the container(5520). As understood by the person skilled in the art, a similarmotorized structure as that of FIG. 55 can be used for a samplepreparation device. In FIG. 55 a heater (5530) is also illustrated onthe external surface of container (5520).

FIG. 56 illustrates another view of the motorized structure of FIG. 55,where two heater plates (5630) are now visible. FIG. 56 also illustratesa reaction chamber (5635).

In some embodiments, the whole sample-to-answer device, comprising areaction cartridge, may be inserted in a sample-to-answer instrument,similar to an optical analysis instrument such as a qPCR instrument, butwith the additional feature of being able to accommodate the entiresample-to-answer device. A sample-to-answer instrument may comprise amotorized structure such as that of FIG. 55, encased in a container box,and may also comprise optical elements to perform optical analysistechniques. For example, a sample-to-answer instrument might comprisethe optical elements as described in FIG. 49, as well as the motorizedstructure to operate plungers as illustrated in FIG. 55.

FIG. 57 illustrates some components of a sample-to-answer instrument.Similarly to FIG. 55, the instrument in FIG. 57 may comprise a motor(5705) and linear actuator (5710) to operate the plungers (5715) of asample-to-answer device (5720). A sample-to-answer device, as describedin the present disclosure, comprises a reaction chamber (5725).

The sample-to-answer instrument may comprise a solenoid (5730) which canoperate a moving plate (5735), similarly to the optical analysisinstrument as illustrated in FIG. 49.

Referring to FIG. 57, the sample-to-answer instrument may comprise anoptical element (5740). Element (5740) may comprise, for example, anintegrated LED light source, a lens and an optical excitation filter. Awaveguide (5745) may guide electromagnetic rays onto the prism ofreaction chamber (5725).

FIG. 58 illustrates some details of the sample-to-answer instrument ofFIG. 57. Referring to FIG. 58, an instrument can comprise a reactionchamber (5805), an optical element (5810) and a waveguide (5815).

FIG. 59 illustrates an alternative view of the instrument of FIG. 57.Referring to FIG. 59, an instrument can comprise a reaction chamber(5905), an optical element (5910) and a waveguide (5915).

FIG. 60 illustrates a top view of the instrument of FIG. 57. Referringto FIG. 60, an instrument can comprise a reaction chamber (6005), anoptical element (6010) and a waveguide (6015).

FIG. 61 illustrates a detailed view of an exemplary optical structurefor the instruments of the present disclosure, for example for theinstrument of FIG. 57. Such optical structure may be used for an opticalanalysis instrument or a sample-to-answer instrument.

Referring to FIG. 61, an optical structure may comprise an LED lightsource (6105), as well as a lens and excitation filter element (6110).In some embodiments, elements (6105) and (6110) may be molded in asingle piece. The optical elements of, for example, FIG. 57, togetherwith the motorized parts of, for example, FIG. 57, may be encased in abox with the necessary electronic control elements and interfaceelements (such as a touchscreen), for a sample-to-answer instrument.Such additional components are illustrated, for example, in FIGS. 49 and54 for other instruments. As understood by the person skilled in theart, such additional components may be similarly designed for differentembodiments and for different instruments, provided that the controlelements are configured to operate the motors and actuators, the opticalelements, or both. As described in the present disclosure, a samplepreparation instrument comprises the motors and actuators; thesample-to-answer instrument comprises motors, actuators and opticalelements; the optical analysis instrument comprises the opticalelements.

The electronic components of the instruments of the present disclosuremay comprise, for example, a microcontroller, such as an ARM, LPC1768,memory, a solenoid interface, such as A4950, heater drivers (such asMOSFETs), USB, Ethernet, Blutooth, Wireless or other communicationinterfaces, motion control sensors to operate plates in contact with areaction cartridge or to operate motors and actuators for the plungers,for example ST L6470, a resistance temperature detector (RTD) interface,such as MAX31866, an interface such as MAX31865, a photodiode interface,such as DDC114, and LED drivers such as CAT4109 or CAT4101. Theinstruments may be controlled, for example through a smartphone, tabletor other portable computing devices and computers.

A portable device for sample preparation or sample-to-answer may befabricated in the shape of a pen. Such device may be highly integratedwith different manual or automatic components. For example, FIG. 62illustrates an exemplary pen-shaped device, in an exploded schematicview.

The device of FIG. 62 may comprise a series of buttons (6205), forexample arranged in a circular pattern on the top of a supportingstructure shaped like a pen (6210). The buttons (6205) may manuallyoperate plungers (6215) in containers (6220). In other embodiments, thebuttons (6205) may activate miniaturized motors or actuators (6225)which can in turn operate on the plungers (6215) automatically. Thecontainers (6220) may be connected to a disk (6230), which may host asample holder such as a DNA membrane (6235). The disk (6230) may alsocomprise functional elements, such as miniaturized filters or mixers(6240). Additional containers may be housed under the disk (6230), forexample waste containers (6245). Such containers may receive the wasteor intermediary products through openings in the disk (6230). One ormore reaction chambers (6250) may be also contained in the pen-shapeddevice (6210). The device may also comprise a needle (6255), which maybe connected to a reservoir (6260). Through the needle (6255), samplesmay be collected, for example blood samples. The needle (6255) may beretractable, or may be fixed in the place at the tip of the pen-shapeddevice (6210). In some embodiments, different needles may be present,and they can in turn be extended through a bottom opening structure(6265) either manually or through miniaturized motors. The samplecollected through the needle (6255) may be transferred to containers atthe top of the device, such as the container (6220), for the necessaryprocessing.

The disk (6230) may comprise a marker which is visible externally to thepen-shaped structure (6210), to allow the user to determine the diskposition. In some embodiments, the marker also has a surface whichallows grip, in order for a user to rotate the disk manually. In someembodiments, buttons (6205) may be positioned on the sides of thepen-shaped structure (6210), and the top of the pen-shaped structure(6210) may comprise a single button to allow movement of fluids, forexample, the single button may comprise a flexible reservoir filled withan elution solution, which is pushed by the user during the elutionstep.

In other embodiments, the motorized actuators (6225) may be controlledby a central microprocessor programmed to perform a desired sequence.

The person skilled in the art will understand that the pen-shaped deviceof FIG. 62 may comprise any of the elements and features described inother devices of the present disclosure, for sample preparation orsample-to-answer. Such device may allow the execution of techniques,such as for example qPCR. A processed sample may be extracted from apen-shaped device in a variety of ways, for example a cartridge may bedetachable from the pen-shaped device upon disassembling of thesupporting structure shaped like a pen (6210). In other embodiments, anelution container may comprise a bottom opening, through which the elutesolution containing the target analyte may be poured out of the bottomopening of a pen-shaped device, for example to be inserted in a reactionchamber. In other embodiments, the elution container may comprise aneedle injector, to facilitate the transfer of the fluid into anexternal reaction chamber. In yet other embodiments, the elutioncontainer may be configured with a capillary to extract a fluid. Inother embodiments, if the pen-shaped device comprises a reactionchamber, a capillary may be attached to the reaction chamber to removethe target analyte from the chamber. In some embodiments, the capillarymay be configured to perform capillary electrophoresis.

In some embodiments of the present disclosure, reaction cartridgescomprise a metallic back plate. The reaction chamber is molded into thepolymeric part of a cartridge. In other embodiments, the reactionchamber may be etched as a space into the metallic back plate. In someembodiments, the reservoir may be 200×3000×4000 micrometers. Thereaction chamber may be etched, molded or embossed into the polymer, orthe metal part of the cartridge. In some embodiments, a flat metal layerand a flat polymer layer may be interspaced by a spacer layer, with thechamber fabricated from an empty space in the spacer layer. The polymerpart of the cartridge may be injection molded. The metal part of thecartridge may be laser cut, cut with a water jet, or mechanical blade.Plasma or solvents may be used for cleaning the parts duringfabrication.

FIG. 63 illustrates different fabrication methods for a reactionchamber. A metal backplate (6305) may be separated by a polymer spacer(6310) from a transparent polymer top (6315). As understood by theperson skilled in the art, every reaction chamber and cartridge asdescribed in the present disclosure may have a transparent top layer, toallow electromagnetic waves to reach the reaction chamber when a lightsource is directed at the prism of a reaction cartridge. In anotherembodiment, the chamber may be within the metal layer (6320), with atransparent polymer (6325) as a top layer. In another embodiment, thechamber may be within the transparent polymer (6340), with a metal layeras a bottom layer (6330).

A number of embodiments of the disclosure have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the presentdisclosure. Accordingly, other embodiments are within the scope of thefollowing claims.

The examples set forth above are provided to those of ordinary skill inthe art a complete disclosure and description of how to make and use theembodiments of the disclosure, and are not intended to limit the scopeof what the inventor/inventors regard as their disclosure.

Modifications of the above-described modes for carrying out the methodsand devices herein disclosed that are obvious to persons of skill in theart are intended to be within the scope of the following claims. Allpatents and publications mentioned in the specification are indicativeof the levels of skill of those skilled in the art to which thedisclosure pertains. All references cited in this disclosure areincorporated by reference to the same extent as if each reference hadbeen incorporated by reference in its entirety individually.

It is to be understood that the disclosure is not limited to particularmethods or devices, which can, of course, vary. It is also to beunderstood that the terminology used herein is for the purpose ofdescribing particular embodiments only, and is not intended to belimiting. As used in this specification and the appended claims, thesingular forms “a,” “an,” and “the” include plural referents unless thecontent clearly dictates otherwise. The term “plurality” includes two ormore referents unless the content clearly dictates otherwise. Unlessdefined otherwise, all technical and scientific terms used herein havethe same meaning as commonly understood by one of ordinary skill in theart to which the disclosure pertains.

What is claimed is:
 1. A device comprising: a top structure, a bottomstructure, and a connecting structure, wherein the connecting structureconnects the top structure to the bottom structure, and wherein I) thetop structure comprises a) a first plurality of containers, eachcontainer of the first plurality of containers having: i) a top opening,wherein the top opening has a sealing element which can slide inside thecontainer while substantially maintaining a seal; ii) a central part;and iii) a bottom opening; b) at least two ports in at least onecontainer of the first plurality of containers, the at least two portscomprising i) a first port configured for air venting; ii) a second portconfigured for fluid insertion; and iii) a sealing cap for each port;II) the bottom structure comprises a) a second plurality of containers,each container of the second plurality of containers having i) a topopening; ii) a central part; and iii) a bottom opening, wherein thebottom opening has a sealing element; and III) the connecting structurecomprises a) at least one fluidics channel; b) a supporting elementwhich can slide, rotate or move within a plane, thereby establishing afluidics connection, through the at least one fluidics channel, betweenthe bottom opening of at least one container of the first plurality ofcontainers and the top opening of at least one container of the secondplurality of containers, while substantially sealing other bottomopenings of the first plurality of containers and other top openings ofthe second plurality of containers.
 2. The device of claim 1, whereinthe first and second plurality of containers are arranged in a circularpattern and the connecting structure is a disk.
 3. The device of claim2, wherein the sealing element of the first plurality of containers is aplunger or a piston.
 4. The device of claim 1, wherein at least onecontainer of the first plurality of containers further comprises anadditional container attached on a central part of the at least onecontainer, the additional container comprising a top opening, whereinthe top opening has a sealing element which can slide inside theadditional container while substantially maintaining a seal; a centralpart; a bottom opening attached to the at least one container of thefirst plurality of containers; and at least two ports in the additionalcontainer, the at least two ports comprising a first port configured forair venting; a second port configured for fluid insertion; a sealing capfor each port.
 5. The device of claim 1, wherein the bottom opening ofthe first plurality of containers and the top opening of the secondplurality of containers comprises a sealing element configured tosubstantially seal a container against the connecting structure; orallow a fluidics connection between the top structure and the bottomstructure, depending on a position of the connecting structure.
 6. Thedevice of claim 4, wherein the additional container further comprisesone or more of a mixer element, a pump element, a lysing element, and afilter element.
 7. The device of claim 1, wherein the connectingstructure further comprises at least one functional element selectedfrom the group consisting of: a nucleic acid binding membrane, a mixer,a sonicating element, and a filter.
 8. The device of claim 1, whereinthe sealing element of the second plurality of containers comprises aspringed seal, a plunger, a piston, or a rubber pouch.
 9. The device ofclaim 1, wherein at least one container of the second plurality ofcontainers further comprises an additional container attached on thecentral part of the at least one container, the additional containercomprising a top opening, wherein the top opening has a sealing elementwhich can slide inside the additional container while substantiallymaintaining a seal; a central part; and a bottom opening attached to theat least one container of the first plurality of containers.
 10. Thedevice of claim 4, wherein the additional container further comprises agrinder element.
 11. The device of claim 1, wherein the second portcomprises a supporting element configured to support a tip of a pipette.12. The device of claim 1, wherein the device comprises a materialselected from a cyclic olefin copolymer or cyclic olefin polymer,thermoplastic materials, metal, glass or elastomers.
 13. The device ofclaim 1, wherein at least one of the first plurality of containerscontains one or more of an elute solution, a washing solution, and alysing solution.
 14. The device of claim 1, wherein at least onecontainer of the first or second plurality of containers has a flattenedcylindrical structure.
 15. The device of claim 1, wherein at least onecontainer of the first or second plurality of containers has a heaterelement attached to an outer surface of the at least one container. 16.The device of claim 1, wherein the second port is attached to acapillary.
 17. A method comprising: providing the device of claim 1;inserting a sample analyte in a first container of the first pluralityof containers; and operating the connecting structure and the sealingelements of the first and second plurality of containers, based on adesired movement of fluids between the first and second plurality ofcontainers, thereby obtaining a prepared sample.
 18. The method of claim17, wherein the desired movement of fluids comprises: a lysing step; atleast one washing step; and an elution step.
 19. The method of claim 17,wherein the prepared sample is for polymerase chain reaction orenzyme-linked immunosorbent assay.